Question about lcr and segdup

KalinNonchev / gnomAD_DB

This package scales the huge gnomAD files to a SQLite database, which is easy and fast to query. It extracts from a gnomAD vcf the minor allele frequency for each variant.

MIT License

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Question about lcr and segdup #34

Closed sophiezhang-origin closed 3 months ago

sophiezhang-origin commented 3 months ago

Hello,

I wonder if it is possible to tell if a variant falls into LCR or SEGDUP region using gnomAD_DB? It seems like the "filter" columns does not contain "lcr" or "seddup" flag.

Any feedback is greatly appreciated. Thank you so much in advance!

KalinNonchev commented 3 months ago

Hello @sophiezhang-origin ,

Thank you for your interest! You can provide the regions and try

db.get_info_for_interval(chrom=21, interval_start=9825780, interval_end=9825799, query="AF")

You can find more information in the tutorial.

Please let me know if you have further questions.

Best,